def setIteration(self, iteration_size: BoundingBox, stride: Vector):
"""
Sets the parameters for iterating through the dataset
:param iteration_size: The size of each data sample in the volume
:param stride: The displacement of each iteration
"""
if not isinstance(iteration_size, BoundingBox):
error_string = ("iteration_size must have type BoundingBox" +
" instead it has type {}")
error_string = error_string.format(type(iteration_size))
raise ValueError(error_string)
if not isinstance(stride, Vector):
raise ValueError("stride must have type Vector")
if not iteration_size.isSubset(
BoundingBox(Vector(0, 0, 0),
self.getBoundingBox().getSize())):
raise ValueError("iteration_size must be smaller than volume size")
self.setIterationSize(iteration_size)
self.setStride(stride)
def ceil(x):
return int(round(x))
self.element_vec = Vector(
*map(lambda L, l, s: ceil((L - l) / s + 1),
self.getBoundingBox().getSize().getComponents(),
self.iteration_size.getSize().getComponents(),
self.stride.getComponents()))
self.index = 0
def setIteration(self, iteration_size: BoundingBox, stride: Vector):
if not isinstance(iteration_size, BoundingBox):
error_string = ("iteration_size must have type BoundingBox" +
" instead it has type {}")
error_string = error_string.format(type(iteration_size))
raise ValueError(error_string)
if not isinstance(stride, Vector):
raise ValueError("stride must have type Vector")
if not iteration_size.isSubset(
BoundingBox(Vector(0, 0, 0),
self.getBoundingBox().getSize())):
raise ValueError(
"iteration_size must be smaller than volume size " +
"instead the iteration size is {} ".format(
iteration_size.getSize()) +
"and the volume size is {}".format(
self.getBoundingBox().getSize()))
self.setIterationSize(iteration_size)
self.setStride(stride)
def ceil(x):
return int(round(x))
self.element_vec = Vector(
*map(lambda L, l, s: ceil((L - l) / s + 1),
self.getBoundingBox().getSize().getComponents(),
self.iteration_size.getSize().getComponents(),
self.stride.getComponents()))
self.index = 0
def getArray(self, bounding_box: BoundingBox = None) -> np.ndarray:
"""
Retrieves the array contents of the volume. If a bounding box is
provided, the subsection is returned.
:param bounding_box: The bounding box of a subsection of the volume.
If the bounding box is outside of the volume, a ValueError is raised.
"""
if bounding_box is None:
return self.array
else:
if not bounding_box.isSubset(self.getBoundingBox()):
raise ValueError("The bounding box must be a subset" +
" of the volume")
centered_bounding_box = bounding_box - self.getBoundingBox(
).getEdges()[0]
edge1, edge2 = centered_bounding_box.getEdges()
x1, y1, z1 = edge1.getComponents()
x2, y2, z2 = edge2.getComponents()
return self.array[z1:z2, y1:y2, x1:x2]